Two types of pairwise genome alignment are available in VectorBase, based on LastZ [1] and translated BLAT (tBLAT) [2]. LastZ is typically used for closely related species, and tBLAT for more distant species. The method of alignment affects the coverage of the genomes, with tBLAT expected to mostly find homologies in coding regions.

The raw results from LastZ or tBLAT are alignment blocks, which are 'chained' according to their location in both genomes, then 'netted' to choose the best sub-chain in each region for the reference species [3].

Data Access

This project has been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN272201400029C.